[BioC] vsn and oligo (or xps?) packages for GeneST expression arrays

[Benilton Carvalho]

Hi Tim,

yes, vsn support is planned. The affy and oligo packages share methods with the same name which come to be a problem when adding support for vsn. We already have agreed on a solution and it's just a matter of implementing these changes, which will greatly simplify this task.

As soon as something is available (on the devel branch), I'll get back to the list.

Cheers,

b

On Jan 4, 2010, at 2:06 PM, Tim Rayner wrote:

> Hi,
> 
> I'm curious to know whether there are any plans to support the use of
> the VSN algorithm (i.e. the vsn package) with the classes defined by
> the oligo package. The reason I ask is that it seems as though the
> latter package is now touted as one of the supported methods of
> handling Affymetrix GeneST expression arrays (e.g. HuGene, MoGene),
> but as far as I can see the only expression
> normalisation/summarisation method currently supported for objects of
> the oligo GeneFeatureSet class seems to be RMA. I'm not even sure if
> GCRMA is supported for GeneFeatureSet objects? I guess the same
> questions also apply to the xps package, although I suspect that VSN
> support would turn out to be more work to implement there given the
> rather different underlying object structures used by xps. Do please
> correct me if I'm wrong about any of this, but until now I've been
> forced to shoehorn our data into the old AffyBatch workflow using
> custom CDFs and I'd like to know if there's a better (i.e. supported)
> workflow I could be using.
> 
> Best regards,
> 
> Tim Rayner
> 
> 
> 
> # Current setup for reference:
>> sessionInfo()
> R version 2.10.0 Patched (2009-11-03 r50305)
> x86_64-apple-darwin9.8.0
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] oligo_1.10.0         preprocessCore_1.8.0 oligoClasses_1.8.0
> [4] gcrma_2.18.0         vsn_3.14.0           affy_1.24.2
> [7] Biobase_2.6.1
> 
> loaded via a namespace (and not attached):
> [1] affxparser_1.18.0 affyio_1.14.0     Biostrings_2.14.8 DBI_0.2-4
> [5] grid_2.10.0       IRanges_1.4.9     lattice_0.17-26   limma_3.2.1
> [9] splines_2.10.0
> 
> 
> 
> --
> Bioinformatician
> Smith Lab, CIMR
> University of Cambridge
> 
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